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--- jvs:fscan:manual:chapter3:winkeys:roi [2011/03/31 14:49] – external edit 127.0.0.1
+++ jvs:fscan:manual:chapter3:winkeys:roi [2024/06/21 15:44] (current) – external edit 127.0.0.1
@@ Line 53: / Line 53: @@
     path -- linked points in space
     polygon -- closed path (perimeter on surface)
-    slice polygons -- separate path drawn in each slice
+    slice polygons -- separate polygon drawn in each slice
-    shell -- pts on perimeter of 3-D region
+    slice paths -- separate path drawn in each slice
     area -- perimeter and all internal points
     shell -- perimeter and all internal points
@@ Line 137: / Line 137: @@
         VAL:  Value to write if (FLG & 4)
 h                auto roi for surfs
-,1h              surf: expand path to geodesic list
+     For surfaces:
-,2h              surf: mark all vertices inside path with parm and color
+,1h            expand path to geodesic list
-,3h              surf: expand path to include all inside vertices
+,2h            mark all vertices inside path with parm and color
-,4h              surf: paint roi color onto vertices
+,3h            expand path to include all inside vertices
+,4h            paint roi color onto vertices
+     For images:
+,1,flg,dist h
+                        expand path by interpolation
+          FLG  1 - reuse same ROI
+- interpolate contours for intervening slices
+               ? - add node for every voxel DIST step (default)
+          DIST   - distance between node steps in mm (default: voxel width)
+                 - Flg 2: distance between contours in mm (default: voxel depth)
+,2,flg,dist,val h
+                        sample image perpendicular to path at each node;
+                        find edge where image intensity crosses VAL boundary,
+                        move node to edge if found; flag nodes where no edge found
+          FLG  1 - reuse same ROI (default is create new ROI)
+- edge is intensity change >= VAL %
+- only look for edge on one side
+                   (default is one side, then the other [left then right])
+- swap search directions (look first on right side of path)
+                   (default is inward for counter-clockwise path)
+- first jump away from search direction then search (assumes 4)
+          VAL  edge intensity value (default current Thresh value, or 1 if Thresh==0)
+,3,flg,dist h	 clean up nodes in path
+          FLG  1 - reuse same ROI (default is create new ROI)
+               ? - remove non-edge nodes (after 10,2h cmd)
+- remove kinks (where path doubles back on itself)
+- remove outliers (where path jumps
+- smooth regardless of distance (default: smooth small jumps)
+          DIST
+,5,flg,val,plane h     Generate contour ROI for image mask(s)
+               This creates a contour around the border of the image
+               region with intensity VAL (each value >0 by default)
+               Note: this is inverse of 9h cmd.
+          FLG  1 - inside voxels have values >= VAL (default)
+- inside voxels have values <= VAL
+- edge is intensity drop >= VAL
+- edge is intensity increase >= VAL
+- edge is intensity drop >= VAL %
+- edge is intensity increase >= VAL %
+          VAL  edge intensity value (default current Thresh value, or 1 if Thresh==0)
+          PLANE is 0,1,2 for which image plane x,y,z to draw contours
+               (plane=2, z, by default.
 h                Sample values in a region (ROI or near cursor)
      'name',11,flg,roinum,dist,thresh h